Package: powerTCR 1.25.0
Hillary Koch
powerTCR: Model-Based Comparative Analysis of the TCR Repertoire
This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.
Authors:
powerTCR_1.25.0.tar.gz
powerTCR_1.25.0.zip(r-4.5)powerTCR_1.25.0.zip(r-4.4)powerTCR_1.25.0.zip(r-4.3)
powerTCR_1.25.0.tgz(r-4.4-any)powerTCR_1.25.0.tgz(r-4.3-any)
powerTCR_1.25.0.tar.gz(r-4.5-noble)powerTCR_1.25.0.tar.gz(r-4.4-noble)
powerTCR_1.25.0.tgz(r-4.4-emscripten)powerTCR_1.25.0.tgz(r-4.3-emscripten)
powerTCR.pdf |powerTCR.html✨
powerTCR/json (API)
NEWS
| # Install 'powerTCR' in R: |
| install.packages('powerTCR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- repertoires - Two toy examples of sample TCR repertoires.
On BioConductor:powerTCR-1.25.0(bioc 3.20)powerTCR-1.24.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:85662011d1
Exports:clusterPlotddiscgammagpdfdespondsfdiscgammagpdget_bootstrapsget_distancesget_diversityget_mleget_nllhJS_despondsJS_distJS_splicedpdiscgammagpdqdiscgammagpdrdiscgammagpd
Dependencies:cliclustercodetoolscubaturedoParallelevdevmixforeachgluegsliteratorslatticelifecyclemagrittrMASSMatrixmgcvnlmepermutepurrrRcpprlangSparseMtruncdistvctrsveganVGAM
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Grab important output from a list of fits | get_diversity get_mle get_nllh |
| Visualize hierarchical clustering of samples | clusterPlot |
| The discrete gamma-GPD spliced threshold distribution | ddiscgammagpd pdiscgammagpd qdiscgammagpd rdiscgammagpd |
| Fit the type-I Pareto distribution as according to Desponds et al. (2016) | fdesponds |
| Fit the discrete gamma-GPD spliced threshold model | fdiscgammagpd |
| Get bootstrapped fits for a list of fitted models | get_bootstraps |
| Compute matrix of pairwise Jensen-Shannon Distances | get_distances |
| Compute the Jensen-Shannon distance between two fitted distributions using the Desponds model | JS_desponds |
| Compute the Jensen-Shannon distance between two model fits | JS_dist |
| Compute the Jensen-Shannon distance between two fitted discrete gamma-GPD spliced threshold distributions | JS_spliced |
| Load in and parse TCR data files for use by powerTCR | parseFile parseFolder |
| Two toy examples of sample TCR repertoires. | repertoires |
